Question: biocLite() fails to install all limma dependencies from CRAN
3
gravatar for Seth Falcon
12.6 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
"Gordon K Smyth" <smyth at="" wehi.edu.au=""> writes: > Hi Jenny, > > statmod is deliberately a "suggests" rather than a "depends" because > only a small number of limma functions use it. > > As far I remember, there the Bioconductor install behaviour hasn't > changed. Maybe I misremember, but I don't think biocLite() has ever > installed suggested packages from CRAN. biocLite has not changed its behavior for this release. However, you can use biocLite to install Suggests. Here are a couple ways to do this: biocLite("limma", dependencies=c("Depends", "Suggests", "Imports")) or simply biocLite("limma", dependencies=TRUE) This has one slight downside: install.packages will install the Suggests for all Depends not just the package you asked for. So you can end up getting many more packages than you really need. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
cancer limma • 3.0k views
ADD COMMENTlink written 12.6 years ago by Seth Falcon7.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 318 users visited in the last hour